Package: vegan 2.7-0
Jari Oksanen
vegan: Community Ecology Package
Ordination methods, diversity analysis and other functions for community and vegetation ecologists.
Authors:
vegan_2.7-0.tar.gz
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vegan.pdf |vegan.html✨
vegan/json (API)
NEWS
| # Install 'vegan' in R: |
| install.packages('vegan', repos = c('https://psolymos.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/vegandevs/vegan/issues
Datasets:
- BCI - Barro Colorado Island Tree Counts
- BCI.env - Barro Colorado Island Tree Counts
- dune - Vegetation and Environment in Dutch Dune Meadows.
- dune.env - Vegetation and Environment in Dutch Dune Meadows.
- dune.phylodis - Taxonomic Classification and Phylogeny of Dune Meadow Species
- dune.taxon - Taxonomic Classification and Phylogeny of Dune Meadow Species
- mite - Oribatid Mite Data with Explanatory Variables
- mite.env - Oribatid Mite Data with Explanatory Variables
- mite.pcnm - Oribatid Mite Data with Explanatory Variables
- mite.xy - Oribatid Mite Data with Explanatory Variables
- pyrifos - Response of Aquatic Invertebrates to Insecticide Treatment
- sipoo - Birds in the Archipelago of Sipoo
- sipoo.map - Birds in the Archipelago of Sipoo
- varechem - Vegetation and environment in lichen pastures
- varespec - Vegetation and environment in lichen pastures
ecological-modellingecologyordination
Last updated 8 days agofrom:18fc5797c2. Checks:OK: 7 NOTE: 2. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 31 2024 |
| R-4.5-win-x86_64 | NOTE | Aug 31 2024 |
| R-4.5-linux-x86_64 | NOTE | Aug 31 2024 |
| R-4.4-win-x86_64 | OK | Aug 31 2024 |
| R-4.4-mac-x86_64 | OK | Aug 31 2024 |
| R-4.4-mac-aarch64 | OK | Aug 31 2024 |
| R-4.3-win-x86_64 | OK | Aug 31 2024 |
| R-4.3-mac-x86_64 | OK | Aug 31 2024 |
| R-4.3-mac-aarch64 | OK | Aug 31 2024 |
Exports:adipartadonisadonis2anosimanova.ccaas.fisheras.mcmc.oecosimuas.mcmc.permatas.mlmas.prestonas.radavgdistbealsbetadisperbetadiverbgdispersalbioenvbioenvdistbstickcacalibratecapscalecascadeKMccaCCorAchaodistcIndexKMclamtestcommsimcommsimulatorcontribdivcoverscalecutreeorddbrdadecobackstanddecoranadecostanddesigndistdesigndist2dispindmorisitadispweightdist2xydistconnecteddiversitydownweightdrarefyeigengradeigenvalsenvfitestaccumRestimateReventstarfactorfitfieller.MOStestfisher.alphafisherfitfitspecaccumgdispweightgoodnesshiersimuindpowerinertcompinitMDSintersetcorisomapisomapdistkendall.globalkendall.postlinestackmake.cepnamesmake.commsimmantelmantel.correlogmantel.partialMDSaddpointsMDSrotatemeandistmetaMDSmetaMDSdistmetaMDSitermetaMDSredistmonoMDSMOStestmrppmsomsoplotmultipartnestedbetajacnestedbetasornestedcheckernesteddiscnestedn0nestednodfnestedtempno.sharednullmodeloecosimuordiareatestordiArrowMulordiarrowsordiArrowTextXYordibarordicloudordiclusterordiellipseordigridordihullordilabelordiplotordipointlabelordiR2stepordiresidsordisegmentsordispiderordisplomordistepordisurforditkplotorditorpordixyplotordiYbarpanel.ordipanel.ordi3dpanel.ordiarrowspasteCallpcapcnmpcopermatfullpermatswappermustatspermutestpoolaccumpostMDSprcprepanel.ordi3dprestondistrprestonfitprocrustesprotestrad.lognormalrad.nullrad.preemptrad.zipfrad.zipfbrotradfitradlatticerankindexrarecurverarefyraresloperaupcrickrdaread.ceprenyirenyiaccumrrarefyRsquareAdjscoresshowvarpartssimpersimpson.unbsmbindspandepthspantreespecaccumspecnumberspecpoolspecpool2vectspecslopespenvcorsppscoressppscores<-SSarrheniusSSgitaySSgleasonSSlomolinostepacrossstressplotswantabascotaxa2disttaxondivetoCodatolerancetreedisttreedivetreeheighttsallistsallisaccumvarpartvectorfitvegandocsvegdistvegemiteveiledspecvif.ccawascoreswcmdscalewisconsin
Design decisions and implementation
Rendered fromdecision-vegan.Rnwusingutils::Sweaveon Aug 31 2024.Last update: 2017-09-18
Started: 2013-08-28
Diversity analysis in vegan
Rendered fromdiversity-vegan.Rnwusingutils::Sweaveon Aug 31 2024.Last update: 2018-01-11
Started: 2013-08-28
Introduction to ordination in vegan
Rendered fromintro-vegan.Rnwusingutils::Sweaveon Aug 31 2024.Last update: 2024-04-09
Started: 2013-08-28
Partition of Variation
Rendered frompartitioning.Rnwusingutils::Sweaveon Aug 31 2024.Last update: 2016-02-28
Started: 2016-02-25
vegan FAQ
Rendered fromFAQ-vegan.Rmdusingknitr::knitron Aug 31 2024.Last update: 2024-04-09
Started: 2016-02-25
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Community Ecology Package: Ordination, Diversity and Dissimilarities | vegan-package vegan |
| Add or Drop Single Terms to a Constrained Ordination Model | add1.cca drop1.cca |
| Additive Diversity Partitioning and Hierarchical Null Model Testing | adipart adipart.default adipart.formula hiersimu hiersimu.default hiersimu.formula |
| Permutational Multivariate Analysis of Variance Using Distance Matrices | adonis2 |
| Analysis of Similarities | anosim plot.anosim summary.anosim |
| Permutation Test for Constrained Correspondence Analysis, Redundancy Analysis and Constrained Analysis of Principal Coordinates | anova.cca permutest permutest.cca |
| Averaged Subsampled Dissimilarity Matrices | avgdist |
| Barro Colorado Island Tree Counts | BCI BCI.env |
| Beals Smoothing and Degree of Absence | beals swan |
| Multivariate homogeneity of groups dispersions (variances) | anova.betadisper betadisper boxplot.betadisper eigenvals.betadisper ordimedian plot.betadisper print.betadisper scores.betadisper TukeyHSD.betadisper |
| Indices of beta Diversity | betadiver plot.betadiver scores.betadiver |
| Coefficients of Biogeographical Dispersal Direction | bgdispersal |
| Best Subset of Environmental Variables with Maximum (Rank) Correlation with Community Dissimilarities | bioenv bioenv.default bioenv.formula bioenvdist summary.bioenv |
| PCA biplot | biplot.cca biplot.rda |
| K-means partitioning using a range of values of K | cascadeKM cIndexKM orderingKM plot.cascadeKM pregraphKM |
| [Partial] [Constrained] Correspondence Analysis and Redundancy Analysis | ca cca cca.default cca.formula pca rda rda.default rda.formula |
| Result Object from Constrained Ordination | cca.object model.frame.cca model.matrix.cca model.matrix.rda ordConstrained ordiYbar print.cca weights.cca weights.decorana weights.rda |
| Canonical Correlation Analysis | biplot.CCorA CCorA |
| Multinomial Species Classification Method (CLAM) | clamtest plot.clamtest summary.clamtest |
| Create an Object for Null Model Algorithms | commsim make.commsim print.commsim |
| Contribution Diversity Approach | contribdiv plot.contribdiv |
| Principal Coordinates Analysis and [Partial] Distance-based Redundancy Analysis | capscale dbrda pco |
| Detrended Correspondence Analysis and Basic Reciprocal Averaging | decorana downweight plot.decorana points.decorana scores.decorana summary.decorana text.decorana |
| Standardization Methods for Community Ecology | decobackstand decostand wisconsin |
| Design your own Dissimilarities | chaodist designdist designdist2 |
| Statistics Resembling Deviance and AIC for Constrained Ordination | deviance.cca deviance.rda extractAIC.cca |
| Morisita index of intraspecific aggregation | dispindmorisita |
| Dispersion-based weighting of species counts | dispweight gdispweight summary.dispweight |
| Connectedness of Dissimilarities | distconnected no.shared |
| Ecological Diversity Indices | diversity fisher.alpha simpson.unb specnumber |
| Vegetation and Environment in Dutch Dune Meadows. | dune dune.env |
| Taxonomic Classification and Phylogeny of Dune Meadow Species | dune.phylodis dune.taxon |
| Extract Eigenvalues from an Ordination Object | eigenvals eigenvals.cca eigenvals.decorana eigenvals.default eigenvals.dudi eigenvals.pca eigenvals.pcnm eigenvals.pco eigenvals.prcomp eigenvals.princomp eigenvals.wcmdscale summary.eigenvals |
| Fits an Environmental Vector or Factor onto an Ordination | envfit envfit.default envfit.formula factorfit labels.envfit plot.envfit scores.envfit vectorfit |
| Scale Parameter at the Minimum of the Tsallis Evenness Profile | eventstar |
| Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data | as.fisher as.preston fisherfit lines.preston lines.prestonfit plot.fisher plot.fisherfit plot.preston plot.prestonfit prestondistr prestonfit veiledspec |
| Diagnostic Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA) | alias.cca goodness goodness.cca inertcomp intersetcor spenvcor vif.cca |
| Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling | goodness.metaMDS goodness.monoMDS stressplot stressplot.default stressplot.monoMDS |
| Indicator Power of Species | indpower |
| Linear Model Diagnostics for Constrained Ordination | cooks.distance.cca df.residual.cca hatvalues.cca hatvalues.rda qr.cca rstandard.cca rstudent.cca sigma.cca SSD.cca vcov.cca |
| Isometric Feature Mapping Ordination | isomap isomapdist plot.isomap summary.isomap |
| Kendall coefficient of concordance | kendall.global kendall.post |
| Plots One-dimensional Diagrams without Overwriting Labels | linestack |
| Abbreviates a Two-Part Botanical or Zoological Latin Name into Character String | make.cepnames |
| Mantel and Partial Mantel Tests for Dissimilarity Matrices | mantel mantel.partial |
| Mantel Correlogram | mantel.correlog plot.mantel.correlog |
| Add New Points to NMDS ordination | dist2xy MDSaddpoints |
| Rotate First MDS Dimension Parallel to an External Variable | MDSrotate |
| Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores | initMDS metaMDS metaMDSdist metaMDSiter metaMDSredist plot.metaMDS points.metaMDS postMDS scores.metaMDS text.metaMDS |
| Oribatid Mite Data with Explanatory Variables | mite mite.env mite.pcnm mite.xy |
| Global and Local Non-metric Multidimensional Scaling and Linear and Hybrid Scaling | monoMDS plot.monoMDS points.monoMDS scores.monoMDS text.monoMDS |
| Mitchell-Olds and Shaw Test for the Location of Quadratic Extreme | confint.MOStest fieller.MOStest MOStest plot.MOStest profile.MOStest |
| Multi Response Permutation Procedure and Mean Dissimilarity Matrix | meandist mrpp plot.meandist summary.meandist |
| Functions for performing and displaying a spatial partitioning of cca or rda results | mso msoplot |
| Multiplicative Diversity Partitioning | multipart multipart.default multipart.formula |
| Nestedness Indices for Communities of Islands or Patches | nestedbetajac nestedbetasor nestedchecker nesteddisc nestedn0 nestednodf nestedtemp plot.nestednodf plot.nestedtemp |
| Extract the Number of Observations from a vegan Fit. | nobs.betadisper nobs.cca nobs.CCorA nobs.decorana nobs.isomap nobs.metaMDS nobs.pcnm nobs.procrustes nobs.rad nobs.varpart nobs.wcmdscale |
| Null Model and Simulation | nullmodel print.nullmodel print.simmat simmat simulate.nullmodel smbind str.nullmodel update.nullmodel |
| Evaluate Statistics with Null Models of Biological Communities | as.ts.oecosimu oecosimu toCoda toCoda.oecosimu |
| Add Arrows and Line Segments to Ordination Diagrams | ordiarrows ordigrid ordisegments |
| Support Functions for Drawing Vectors | ordiArrowMul ordiArrowTextXY |
| Display Groups or Factor Levels in Ordination Diagrams | ordiareatest ordibar ordicluster ordiellipse ordihull ordispider scores.ordihull summary.ordiellipse summary.ordihull |
| Add Text on Non-transparent Label to an Ordination Plot. | ordilabel |
| Alternative plot and identify Functions for Ordination | identify.ordiplot ordiplot points.ordiplot scores.ordiplot text.ordiplot |
| Ordination Plots with Points and Optimized Locations for Text | labels.ordipointlabel ordipointlabel plot.ordipointlabel |
| Plots of Residuals and Fitted Values for Constrained Ordination | ordiresids |
| Choose a Model by Permutation Tests in Constrained Ordination | ordiR2step ordistep |
| Fit and Plot Smooth Surfaces of Variables on Ordination. | calibrate.ordisurf ordisurf ordisurf.default ordisurf.formula plot.ordisurf |
| Add Text or Points to Ordination Plots | orditorp |
| Trellis (Lattice) Plots for Ordination | ordicloud ordilattice.getEnvfit ordisplom ordixyplot panel.ordi panel.ordi3d panel.ordiarrows prepanel.ordi3d |
| Principal Coordinates of Neighbourhood Matrix | pcnm scores.pcnm |
| Matrix Permutation Algorithms for Presence-Absence and Count Data | as.ts.permat lines.permat permatfull permatswap plot.permat print.permat print.summary.permat summary.permat toCoda.permat |
| Extract, Analyse and Display Permutation Results | boxplot.permustats c.permustats density.permustats densityplot.permustats pairs.permustats permustats permustats.anosim permustats.anova.cca permustats.CCorA permustats.envfit permustats.factorfit permustats.mantel permustats.mrpp permustats.mso permustats.oecosimu permustats.ordiareatest permustats.permutest.betadisper permustats.permutest.cca permustats.protest permustats.vectorfit qqmath.permustats qqnorm.permustats summary.permustats |
| Permutation tests in Vegan | permutations |
| Permutation test of multivariate homogeneity of groups dispersions (variances) | permutest.betadisper |
| Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis | labels.cca plot.cca points.cca print.summary.cca scores.cca scores.rda summary.cca text.cca |
| Principal Response Curves for Treatments with Repeated Observations | plot.prc prc summary.prc |
| Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA) | calibrate calibrate.cca coef.cca coef.rda fitted.capscale fitted.cca fitted.dbrda fitted.rda predict.cca predict.dbrda predict.decorana predict.rda residuals.cca |
| Procrustes Rotation of Two Configurations and PROTEST | fitted.procrustes lines.procrustes plot.procrustes points.procrustes predict.procrustes procrustes protest residuals.procrustes summary.procrustes text.procrustes |
| Response of Aquatic Invertebrates to Insecticide Treatment | pyrifos |
| Rank - Abundance or Dominance / Diversity Models | AIC.radfit AIC.radfit.frame as.rad coef.radfit coef.radfit.frame deviance.radfit deviance.radfit.frame fitted.radfit fitted.radfit.frame lines.radfit lines.radline logLik, radfit logLik, radfit.frame plot.rad plot.radfit plot.radfit.frame plot.radline points.radfit points.radline predict.radfit predict.radfit.frame predict.radline rad.lognormal rad.null rad.preempt rad.zipf rad.zipfbrot radfit radfit.data.frame radfit.default radlattice summary.radfit.frame |
| Compares Dissimilarity Indices for Gradient Detection | rankindex |
| Rarefaction Species Richness | drarefy rarecurve rarefy rareslope rrarefy |
| Raup-Crick Dissimilarity with Unequal Sampling Densities of Species | raupcrick |
| Reads a CEP (Canoco) data file | read.cep |
| Renyi and Hill Diversities and Corresponding Accumulation Curves | persp.renyiaccum plot.renyi plot.renyiaccum renyi renyiaccum |
| Reorder a Hierarchical Clustering Tree | cutreeord reorder.hclust rev.hclust scores.hclust |
| Adjusted R-square | RsquareAdj RsquareAdj.cca RsquareAdj.default RsquareAdj.glm RsquareAdj.lm RsquareAdj.rda |
| Get Species or Site Scores from an Ordination | scores scores.default scores.lda |
| Screeplots for Ordination Results and Broken Stick Distributions | bstick bstick.cca bstick.decorana bstick.default bstick.prcomp bstick.princomp screeplot.cca screeplot.decorana screeplot.prcomp screeplot.princomp |
| Similarity Percentages | simper summary.simper |
| Simulate Responses with Gaussian Error or Permuted Residuals for Constrained Ordination | simulate.capscale simulate.cca simulate.rda |
| Birds in the Archipelago of Sipoo (Sibbo and Borgå) | sipoo sipoo.map |
| Minimum Spanning Tree | as.hclust.spantree cophenetic.spantree lines.spantree plot.spantree spandepth spantree |
| Species Accumulation Curves | AIC.fitspecaccum boxplot.specaccum deviance.fitspecaccum fitspecaccum lines.fitspecaccum lines.specaccum logLik.fitspecaccum nobs.fitspecaccum plot.fitspecaccum plot.specaccum predict.fitspecaccum predict.specaccum print.specaccum specaccum specslope summary.specaccum |
| Extrapolated Species Richness in a Species Pool | estaccumR estimateR estimateR.data.frame estimateR.default estimateR.matrix plot.poolaccum poolaccum specpool specpool2vect summary.poolaccum |
| Add or Replace Species Scores in Distance-Based Ordination | sppscores sppscores<- sppscores<-.capscale sppscores<-.dbrda sppscores<-.metaMDS sppscores<-.monoMDS sppscores<-.wcmdscale |
| Self-Starting nls Species-Area Models | SSarrhenius SSgitay SSgleason SSlomolino |
| Stepacross as Flexible Shortest Paths or Extended Dissimilarities | stepacross |
| Display Ordination Distances Against Observed Distances in Eigenvector Ordinations | stressplot.capscale stressplot.cca stressplot.dbrda stressplot.prcomp stressplot.princomp stressplot.rda stressplot.wcmdscale |
| Indices of Taxonomic Diversity and Distinctness | plot.taxondive summary.taxondive taxa2dist taxondive |
| Species tolerances and sample heterogeneities | tolerance tolerance.cca tolerance.decorana |
| Functional Diversity and Community Distances from Species Trees | treedist treedive treeheight |
| Tsallis Diversity and Corresponding Accumulation Curves | persp.tsallisaccum tsallis tsallisaccum |
| Vegetation and environment in lichen pastures | varechem varespec |
| Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices | plot.varpart plot.varpart234 showvarparts simpleDBRDA simpleRDA2 summary.varpart varpart varpart2 varpart3 varpart4 |
| Deprecated Functions in vegan package | as.mcmc.oecosimu as.mcmc.permat orditkplot vegan-deprecated |
| Dissimilarity Indices for Community Ecologists | vegdist |
| Display Compact Ordered Community Tables | coverscale tabasco vegemite |
| Weighted Averages Scores for Species | eigengrad wascores |
| Weighted Classical (Metric) Multidimensional Scaling | plot.wcmdscale scores.wcmdscale wcmdscale |
